docs: def read_total_energies(pathname,colnum):
      """Reads in the TEMP#/ener_box#.output file and parses it, returning an array of energies
  
      ARGUMENTS
          filename (string) - the path to the folder of the simulation
  	colnum (integer) column the energy is found in
      """
  
      print("--Reading total energies from %s/..." % pathname)
  
      # Initialize Return variables
      E_kn = numpy.zeros([NumTemps, NumIterations], numpy.float64)
      
      #Read files
      for k in range(NumTemps):
          #Construct each TEMP#/ener_box#.output name and read in the file
          filename = os.path.join(pathname,'TEMP' + str(k), 'ener_box'+ str(k) + '.output')
          infile = open(filename, 'r')
          lines = infile.readlines()
          infile.close()
          numLines = len(lines)
  
          #Initialize arrays for E
          E_from_file = numpy.zeros(NumIterations, numpy.float64)
  
          #Parse lines in each file
          for n in range(NumIterations):
              m = numLines - 2 - n #Count down (the 2 is for index purposes(1) and to not use the double-counted last line (1))
              elements = lines[m].split()
              E_from_file[n] = float(elements[colnum])
  
          #Add in the E's for each timestep (n) at this temperature (k)
          E_kn[k] = E_from_file;
      return E_kn